time-series

Description

The Morphonet Python API provide an easy interface to interact directly with the MorphoNet server. Very useful to upload, download your dataset and superimpose on it any quantitative and quantitative informations.

Description

MorphoNet is a novel concept of web-based morphodynamic browser to visualise and interact with complex datasets, with applications in research and teaching. 

MorphoNet offers a comprehensive palette of interactions to explore the structure, dynamics and variability of biological shapes and its connection to genetic expressions. 

By handling a broad range of natural or simulated morphological data, it fills a gap which has until now limited the quantitative understanding of morphodynamics and its genetic underpinnings by contributing to the creation of ever-growing morphological atlases.

Description

Cell tracking using MU-Lux-CZ algorithm. Dockerized Workflow for BIAFLOWS implemented by Martin Maska (Masaryk University).

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Description

Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version.

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Description

Object tracking. For each time-frame, an image mask is obtained from median filtering (user defined radius), thresholding (user defined level) and hole filling. Convex objects are split apart by distance map watershed from regional intensity maxima (user defined noise tolerance), eroded (user defined radius) and analyzed as 3D particles (assuming some overlap between objects from a frame to the next frame). Finally, division events are analyzed and accounted for to relabel objects.

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